Identifying spatial heterogeneity of sea ice algae communities is critical to predicting ecosystem response under future climate scenarios. Using an autonomous robotic sampling platform beneath sea ice in McMurdo Sound, Antarctica, we measured irradiance in spectral bands expected to describe the spatial heterogeneity. Derived estimates of ice algae biomass identified patchiness at length scales varying from 50&ndash;70&thinsp;m under first-year sea ice. These results demonstrate that a step-change in how these communities can be assessed and monitored. The developed methodologies could be subsequently refined to further categorize different ice algae communities and their associated productivity in both Arctic and Antarctic waters.